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Unabble to load some packages in Rstudio interface while it works on Jupyter Lab #4

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CVandiedonck opened this issue Apr 14, 2022 · 4 comments

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@CVandiedonck
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Bug:

1. When loading an environment with this template (and all other environments I tested with an R kernel), it is impossible in the RStudio interface to load tidyverse package with the R console...

Capture1

2. ...whereas there is not such issue using Jupyter Lab interface:

Capture2

3. Similarly, when using the RStudio interface and a Rmardown file (cf. next paragraph), the error still occurs when running the chunk to load tidyverse
image
Need mardown package to test this point cf https://github.com/CVandiedonck/template-r/tree/patch-2

4. But suprinsingly, the error does not longer occur when knitting a .Rmd document.
image

5. The generated .html file is fine and the sessionInfo() command output shows tidyverse was well loaded (but readxl is not).
Capture5

Description of the error and extension to other packages

The error indicates an issue when trying to load the readxl package which is part of the tidyverse package. The same error occurs when trying to load this package on its own, as well as several other packages that are installed with this "tempalte-r" in the environment, some being very useful like devtools:

  • bslib
  • devtools
  • isoland
  • later
  • pkgload
  • promises
  • rcpp
  • rematch
  • sass
  • testhat
  • vroom
  • data.table

Question @plasmabio/quantstack

Is this an issue in Plasma, something missing in the configuration files of the template or an issue with the Ubuntu server?
For the server, I tried on different instances (adenine or uracile at Université Paris Cité) or the VM machine you granted us acess too. The screenshots were generated with this VM.

@pierrepo
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pierrepo commented Apr 14, 2022

This issue might be related to this discussion and this one "libstdc++.so.6: version `GLIBCXX_3.4.26' not found on Linux"

@pierrepo
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pierrepo commented Apr 20, 2022

This bug is also obtained with repo2docker. I created the corresponding issue jupyterhub/repo2docker#1153

For troubleshooting, these commands are useful:

library(tidyverse)
sessionInfo()
Sys.getenv("LD_LIBRARY_PATH")

@jtpio
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jtpio commented Nov 20, 2023

I just checked with the latest repo2docker and the troubleshooting steps mentioned above, and it looks like it is working fine now?

image

So hopefully this issue will be fixed by plasmabio/plasma#217, which updates to the latest repo2docker image.

@CVandiedonck
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Yes it is all fixed with the update of repo2docker. We checked this during the summer and forgot to close the issue. It has been working well since.

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3 participants